Workflow: Seurat Cluster
Seurat Cluster ============== Runs filtering, integration, and clustering analyses for Cell Ranger Count Gene Expression or Cell Ranger Aggregate experiments.
- Selected
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- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Inputs
ID | Type | Title | Doc |
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alias | String | Experiment short name/Alias | |
no_sct | Boolean (Optional) | Use LogNormalize instead of SCTransform when integrating datasets |
Do not use SCTransform when running datasets integration. Use LogNormalize instead. |
species | Species for gene name conversion when running cell type prediction |
Select species for gene name conversion when running cell type prediction with Garnett classifier. If \"none\" - do not convert gene names |
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threads | Integer (Optional) | Threads number to use |
Threads number |
test_use | Statistical test to use for gene markers identification |
Statistical test to use for gene markers identification. |
|
resolution | String (Optional) | Comma or space separated list of clustering resolutions |
Comma or space separated list of clustering resolutions |
minimum_pct | Float (Optional) | Include only those genes that are detected in not lower than this fraction of cells in either of the two tested clusters |
Include only those genes that are detected in not lower than this fraction of cells in either of the two tested clusters. |
umap_method | UMAP implementation to run |
UMAP implementation to run. |
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umap_metric | The metric to use to compute distances in high dimensional space for UMAP |
The metric to use to compute distances in high dimensional space for UMAP. |
|
umap_spread | Float (Optional) | Effective scale of embedded points on UMAP. Determines how clustered/clumped the embedded points are. |
The effective scale of embedded points on UMAP. In combination with mindist this determines how clustered/clumped the embedded points are. |
minimum_umis | String (Optional) | Include cells where at least this many UMIs are detected |
Include cells where at least this many UMIs are detected. If multiple values provided each of them will be applied to the correspondent dataset. |
mito_pattern | String (Optional) | Pattern to identify mitochondrial genes |
Pattern to identify mitochondrial genes. |
umap_mindist | Float (Optional) | Controls how tightly the embedding is allowed compress points together on UMAP. Sensible values are in the range 0.001 to 0.5 |
Controls how tightly the embedding is allowed compress points together on UMAP. Larger values ensure embedded points are moreevenly distributed, while smaller values allow the algorithm to optimise more accurately with regard to local structure. Sensible values are in the range 0.001 to 0.5. |
barcodes_data | File (Optional) | Headerless TSV/CSV file with cell barcodes (one barcode per line) to prefilter input data |
Path to the headerless TSV/CSV file with selected barcodes (one per line) to prefilter input feature-barcode matrices. If not provided, use all cells |
minimum_cells | Integer (Optional) | Include genes detected in at least this many cells |
Include genes detected in at least this many cells (applied to thoughout all datasets together). |
minimum_logfc | Float (Optional) | Include only those genes that on average have log fold change difference in expression between every tested pair of clusters not lower than this value |
Include only those genes that on average have log fold change difference in expression between every tested pair of clusters not lower than this value. |
classifier_rds | File (Optional) | Garnett classifier rds file for cell type prediction |
Path to the Garnett classifier rds file for cell type prediction. If not provided, skip cell type prediction |
cluster_metric | Distance metric used by the nearest neighbors algorithm when running clustering |
Distance metric used by the nearest neighbors algorithm when running clustering. |
|
dimensionality | Integer (Optional) | Number of principal components to use in UMAP projection and clustering (from 1 to 50) |
Number of principal components to use in UMAP projection and clustering (from 1 to 50). Use Elbow plot to adjust this parameter. |
cell_cycle_data | File (Optional) | TSV/CSV file with cell cycle data with 'phase' and 'gene_id' columns |
TSV/CSV file with cell cycle data. First column - 'phase', second column 'gene_id'. If not provided, skip cell cycle score assignment |
conditions_data | File (Optional) | TSV/CSV file to define datasets conditions with 'library_id' and 'condition' columns. Rows order should correspond to the aggregation metadata. |
Path to the TSV/CSV file to define datasets grouping. First column - 'library_id' with the values provided in the same order as in the correspondent column of the --identity file, second column 'condition'. If not provided, each dataset is assigned to its own biological condition |
umap_nneighbors | Integer (Optional) | Number of neighboring points used in UMAP. Larger values result in loss of detailed local structure. |
Determines the number of neighboring points used in UMAP. Larger values will result in more global structure being preserved at the loss of detailed local structure. In general this parameter should often be in the range 5 to 50. |
maximum_features | String (Optional) | Include cells with the number of genes not bigger than this value |
Include cells with the number of genes not bigger than this value. If multiple values provided each of them will be applied to the correspondent dataset. |
minimum_features | String (Optional) | Include cells where at least this many genes are detected |
Include cells where at least this many genes are detected. If multiple values provided each of them will be applied to the correspondent dataset. |
maximum_mito_perc | Float (Optional) | Include cells with the percentage of transcripts mapped to mitochondrial genes not bigger than this value |
Include cells with the percentage of transcripts mapped to mitochondrial genes not bigger than this value. |
regress_cellcycle | Boolean (Optional) | Regress cell cycle as a confounding source of variation |
Regress cell cycle as a confounding source of variation. |
regress_mito_perc | Boolean (Optional) | Regress mitochondrial gene expression as a confounding source of variation |
Regress mitochondrial gene expression as a confounding source of variation. |
selected_features | String (Optional) | Comma or space separated list of genes of interest |
Comma or space separated list of genes of interest. Default: do not highlight any features |
aggregation_metadata | File | scRNA-Seq Cellranger Aggregate Experiment |
Aggregation metadata in CSV format |
minimum_novelty_score | String (Optional) | Include cells with the novelty score (the ratio of genes per cell over UMIs per cell) not lower than this value |
Include cells with the novelty score (the ratio of genes per cell over UMIs per cell) not lower than this value (calculated as log10(genes)/log10(UMIs)). If multiple values provided each of them will be applied to the correspondent dataset. |
only_positive_markers | Boolean (Optional) | Report only positive gene markers |
Report only positive gene markers. |
high_var_features_count | Integer (Optional) | Number of highly variable genes to detect (used for dataset integration and dimensional reduction) |
Number of highly variable genes to detect (used for dataset integration and dimensional reduction). |
filtered_feature_bc_matrix_folder | File | scRNA-Seq Cellranger Aggregate Experiment |
Compressed folder with aggregated filtered feature-barcode matrices in MEX format |
Steps
ID | Runs | Label | Doc |
---|---|---|---|
seurat_cluster |
../tools/seurat-cluster.cwl
(CommandLineTool)
|
Seurat cluster |
Seurat cluster
============== |
uncompress_feature_bc_matrices |
seurat-cluster.cwl#uncompress_feature_bc_matrices/e1eb561b-f42c-4dae-b083-bd589b529e92
(CommandLineTool)
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compress_cellbrowser_config_data |
../tools/tar-compress.cwl
(CommandLineTool)
|
Compresses input directory to tar.gz |
Outputs
ID | Type | Label | Doc |
---|---|---|---|
ntgr_pca_plot_pdf | File (Optional) | PCA of filtered integrated/scaled datasets |
PCA of filtered integrated/scaled datasets. PDF format |
ntgr_pca_plot_png | File (Optional) | PCA of filtered integrated/scaled datasets |
PCA of filtered integrated/scaled datasets. PNG format |
ntgr_elbow_plot_pdf | File (Optional) | Elbow plot from PCA of filtered integrated/scaled datasets |
Elbow plot from PCA of filtered integrated/scaled datasets. PDF format |
ntgr_elbow_plot_png | File (Optional) | Elbow plot from PCA of filtered integrated/scaled datasets |
Elbow plot from PCA of filtered integrated/scaled datasets. PNG format |
ntgr_pca_heatmap_pdf | File (Optional) | Genes per cells expression heatmap sorted by their PC scores from PCA of filtered integrated/scaled datasets |
Genes per cells expression heatmap sorted by their PC scores from PCA of filtered integrated/scaled datasets. PDF format |
ntgr_pca_heatmap_png | File (Optional) | Genes per cells expression heatmap sorted by their PC scores from PCA of filtered integrated/scaled datasets |
Genes per cells expression heatmap sorted by their PC scores from PCA of filtered integrated/scaled datasets. PNG format |
seurat_clst_data_rds | File | Clustered filtered integrated/scaled Seurat data |
Clustered filtered integrated Seurat data. RDS format |
cellbrowser_html_data | Directory | Directory with UCSC Cellbrowser formatted html data |
Directory with UCSC Cellbrowser formatted html data |
cellbrowser_html_file | File | Open in UCSC Cell Browser |
HTML index file from the directory with UCSC Cellbrowser formatted html data |
raw_qc_mtrcs_plot_pdf | File (Optional) | QC metrics densities per cell (not filtered) |
QC metrics densities per cell (not filtered). PDF format |
raw_qc_mtrcs_plot_png | File (Optional) | QC metrics densities per cell (not filtered) |
QC metrics densities per cell (not filtered). PNG format |
clst_pttv_gene_markers | File | Putative gene markers file for all clusters and all resolutions |
Putative gene markers file for all clusters and all resolutions. TSV format |
clst_umap_res_plot_pdf | File[] (Optional) | Clustered UMAP projected PCA of filtered integrated/scaled datasets |
Clustered UMAP projected PCA of filtered integrated/scaled datasets. PDF format |
clst_umap_res_plot_png | File[] (Optional) | Clustered UMAP projected PCA of filtered integrated/scaled datasets |
Clustered UMAP projected PCA of filtered integrated/scaled datasets. PNG format |
fltr_qc_mtrcs_plot_pdf | File (Optional) | QC metrics densities per cell (filtered) |
QC metrics densities per cell (filtered). PDF format |
fltr_qc_mtrcs_plot_png | File (Optional) | QC metrics densities per cell (filtered) |
QC metrics densities per cell (filtered). PNG format |
clst_csrvd_gene_markers | File | Conserved gene markers file for all clusters and all resolutions |
Conserved gene markers file for all clusters and all resolutions. TSV format |
raw_cell_count_plot_pdf | File (Optional) | Number of cells per dataset (not filtered) |
Number of cells per dataset (not filtered). PDF format |
raw_cell_count_plot_png | File (Optional) | Number of cells per dataset (not filtered) |
Number of cells per dataset (not filtered). PNG format |
fltr_cell_count_plot_pdf | File (Optional) | Number of cells per dataset (filtered) |
Number of cells per dataset (filtered). PDF format |
fltr_cell_count_plot_png | File (Optional) | Number of cells per dataset (filtered) |
Number of cells per dataset (filtered). PNG format |
seurat_cluster_stderr_log | File | stderr log generated by Seurat |
stderr log generated by Seurat |
seurat_cluster_stdout_log | File | stdout log generated by Seurat |
stdout log generated by Seurat |
clst_qc_mtrcs_res_plot_pdf | File[] (Optional) | QC metrics for clustered UMAP projected PCA of filtered integrated/scaled datasets |
QC metrics for clustered UMAP projected PCA of filtered integrated/scaled datasets. PDF format |
clst_qc_mtrcs_res_plot_png | File[] (Optional) | QC metrics for clustered UMAP projected PCA of filtered integrated/scaled datasets |
QC metrics for clustered UMAP projected PCA of filtered integrated/scaled datasets. PNG format |
ntgr_pca_loadings_plot_pdf | File (Optional) | PC scores of the most variant genes from PCA of filtered integrated/scaled datasets |
PC scores of the most variant genes from PCA of filtered integrated/scaled datasets. PDF format |
ntgr_pca_loadings_plot_png | File (Optional) | PC scores of the most variant genes from PCA of filtered integrated/scaled datasets |
PC scores of the most variant genes from PCA of filtered integrated/scaled datasets. PNG format |
fltr_pca_spl_by_ph_plot_pdf | File (Optional) | Split by cell cycle phase PCA of filtered unintegrated/scaled datasets |
Split by cell cycle phase PCA of filtered unintegrated/scaled datasets. PDF format |
fltr_pca_spl_by_ph_plot_png | File (Optional) | Split by cell cycle phase PCA of filtered unintegrated/scaled datasets |
Split by cell cycle phase PCA of filtered unintegrated/scaled datasets. PNG format |
clst_umap_ctype_res_plot_pdf | File[] (Optional) | Grouped by predicted cell types UMAP projected PCA of filtered integrated/scaled datasets |
Grouped by predicted cell types UMAP projected PCA of filtered integrated/scaled datasets. PDF format |
clst_umap_ctype_res_plot_png | File[] (Optional) | Grouped by predicted cell types UMAP projected PCA of filtered integrated/scaled datasets |
Grouped by predicted cell types UMAP projected PCA of filtered integrated/scaled datasets. PNG format |
expr_avg_per_clst_res_plot_pdf | File[] (Optional) | Scaled average log normalized gene expression per cluster of filtered integrated/scaled datasets |
Scaled average log normalized gene expression per cluster of filtered integrated/scaled datasets. PDF format |
expr_avg_per_clst_res_plot_png | File[] (Optional) | Scaled average log normalized gene expression per cluster of filtered integrated/scaled datasets |
Scaled average log normalized gene expression per cluster of filtered integrated/scaled datasets. PNG format |
expr_clst_heatmap_res_plot_pdf | File[] (Optional) | Log normalized gene expression heatmap of clustered filtered integrated/scaled datasets |
Log normalized gene expression heatmap of clustered filtered integrated/scaled datasets. PDF format |
expr_clst_heatmap_res_plot_png | File[] (Optional) | Log normalized gene expression heatmap of clustered filtered integrated/scaled datasets |
Log normalized gene expression heatmap of clustered filtered integrated/scaled datasets. PNG format |
fltr_umap_spl_by_idnt_plot_pdf | File (Optional) | Split by identity UMAP projected PCA of filtered unintegrated/scaled datasets |
Split by identity UMAP projected PCA of filtered unintegrated/scaled datasets. PDF format |
fltr_umap_spl_by_idnt_plot_png | File (Optional) | Split by identity UMAP projected PCA of filtered unintegrated/scaled datasets |
Split by identity UMAP projected PCA of filtered unintegrated/scaled datasets. PNG format |
ntgr_umap_spl_by_idnt_plot_pdf | File (Optional) | Split by identity UMAP projected PCA of filtered integrated/scaled datasets |
Split by identity UMAP projected PCA of filtered integrated/scaled datasets. PDF format |
ntgr_umap_spl_by_idnt_plot_png | File (Optional) | Split by identity UMAP projected PCA of filtered integrated/scaled datasets |
Split by identity UMAP projected PCA of filtered integrated/scaled datasets. PNG format |
expr_avg_per_ctype_res_plot_pdf | File[] (Optional) | Scaled average log normalized gene expression per predicted cell type of filtered integrated/scaled datasets |
Scaled average log normalized gene expression per predicted cell type of filtered integrated/scaled datasets. PDF format |
expr_avg_per_ctype_res_plot_png | File[] (Optional) | Scaled average log normalized gene expression per predicted cell type of filtered integrated/scaled datasets |
Scaled average log normalized gene expression per predicted cell type of filtered integrated/scaled datasets. PNG format |
expr_ctype_heatmap_res_plot_pdf | File[] (Optional) | Log normalized gene expression heatmap of clustered filtered integrated/scaled datasets with predicted cell types |
Log normalized gene expression heatmap of clustered filtered integrated/scaled datasets with predicted cell types. PDF format |
expr_ctype_heatmap_res_plot_png | File[] (Optional) | Log normalized gene expression heatmap of clustered filtered integrated/scaled datasets with predicted cell types |
Log normalized gene expression heatmap of clustered filtered integrated/scaled datasets with predicted cell types. PNG format |
expr_dnst_per_clst_res_plot_pdf | File[] (Optional) | Log normalized gene expression densities per cluster of filtered integrated/scaled datasets |
Log normalized gene expression densities per cluster of filtered integrated/scaled datasets. PDF format |
expr_dnst_per_clst_res_plot_png | File[] (Optional) | Log normalized gene expression densities per cluster of filtered integrated/scaled datasets |
Log normalized gene expression densities per cluster of filtered integrated/scaled datasets. PNG format |
expr_per_clst_cell_res_plot_pdf | File[] (Optional) | Log normalized gene expression per cell of clustered filtered integrated/scaled datasets |
Log normalized gene expression per cell of clustered filtered integrated/scaled datasets. PDF format |
expr_per_clst_cell_res_plot_png | File[] (Optional) | Log normalized gene expression per cell of clustered filtered integrated/scaled datasets |
Log normalized gene expression per cell of clustered filtered integrated/scaled datasets. PNG format |
clst_umap_spl_by_ph_res_plot_pdf | File[] (Optional) | Split by cell cycle phase clustered UMAP projected PCA of filtered integrated/scaled datasets |
Split by cell cycle phase clustered UMAP projected PCA of filtered integrated/scaled datasets. PDF format |
clst_umap_spl_by_ph_res_plot_png | File[] (Optional) | Split by cell cycle phase clustered UMAP projected PCA of filtered integrated/scaled datasets |
Split by cell cycle phase clustered UMAP projected PCA of filtered integrated/scaled datasets. PNG format |
expr_dnst_per_ctype_res_plot_pdf | File[] (Optional) | Log normalized gene expression densities per predicted cell type of filtered integrated/scaled datasets |
Log normalized gene expression densities per predicted cell type of filtered integrated/scaled datasets. PDF format |
expr_dnst_per_ctype_res_plot_png | File[] (Optional) | Log normalized gene expression densities per predicted cell type of filtered integrated/scaled datasets |
Log normalized gene expression densities per predicted cell type of filtered integrated/scaled datasets. PNG format |
expr_per_ctype_cell_res_plot_pdf | File[] (Optional) | Log normalized gene expression per cell of clustered filtered integrated/scaled datasets with predicted cell types |
Log normalized gene expression per cell of clustered filtered integrated/scaled datasets with predicted cell types. PDF format |
expr_per_ctype_cell_res_plot_png | File[] (Optional) | Log normalized gene expression per cell of clustered filtered integrated/scaled datasets with predicted cell types |
Log normalized gene expression per cell of clustered filtered/scaled integrated datasets with predicted cell types. PNG format |
raw_qc_mtrcs_gr_by_cond_plot_pdf | File (Optional) | Grouped by condition QC metrics densities per cell (not filtered) |
Grouped by condition QC metrics densities per cell (not filtered). PDF format |
raw_qc_mtrcs_gr_by_cond_plot_png | File (Optional) | Grouped by condition QC metrics densities per cell (not filtered) |
Grouped by condition QC metrics densities per cell (not filtered). PNG format |
fltr_qc_mtrcs_gr_by_cond_plot_pdf | File (Optional) | Grouped by condition QC metrics densities per cell (filtered) |
Grouped by condition QC metrics densities per cell (filtered). PDF format |
fltr_qc_mtrcs_gr_by_cond_plot_png | File (Optional) | Grouped by condition QC metrics densities per cell (filtered) |
Grouped by condition QC metrics densities per cell (filtered). PDF format |
raw_umi_dnst_spl_by_cond_plot_pdf | File (Optional) | Split by condition UMI density per cell (not filtered) |
Split by condition UMI density per cell (not filtered). PDF format |
raw_umi_dnst_spl_by_cond_plot_png | File (Optional) | Split by condition UMI density per cell (not filtered) |
Split by condition UMI density per cell (not filtered). PNG format |
clst_umap_spl_by_cond_res_plot_pdf | File[] (Optional) | Split by condition clustered UMAP projected PCA of filtered integrated/scaled datasets |
Split by condition clustered UMAP projected PCA of filtered integrated/scaled datasets. PDF format |
clst_umap_spl_by_cond_res_plot_png | File[] (Optional) | Split by condition clustered UMAP projected PCA of filtered integrated/scaled datasets |
Split by condition clustered UMAP projected PCA of filtered integrated/scaled datasets. PNG format |
compressed_cellbrowser_config_data | File | Compressed directory with UCSC Cellbrowser configuration data |
Compressed directory with UCSC Cellbrowser configuration data |
fltr_pca_spl_by_mito_perc_plot_pdf | File (Optional) | Split by level of transcripts mapped to mitochondrial genes PCA of filtered unintegrated/scaled datasets |
Split by level of transcripts mapped to mitochondrial genes PCA of filtered unintegrated/scaled datasets. PDF format |
fltr_pca_spl_by_mito_perc_plot_png | File (Optional) | Split by level of transcripts mapped to mitochondrial genes PCA of filtered unintegrated/scaled datasets |
Split by level of transcripts mapped to mitochondrial genes PCA of filtered unintegrated/scaled datasets. PNG format |
fltr_umi_dnst_spl_by_cond_plot_pdf | File (Optional) | Split by condition UMI density per cell (filtered) |
Split by condition UMI density per cell (filtered). PDF format |
fltr_umi_dnst_spl_by_cond_plot_png | File (Optional) | Split by condition UMI density per cell (filtered) |
Split by condition UMI density per cell (filtered). PNG format |
raw_gene_dnst_spl_by_cond_plot_pdf | File (Optional) | Split by condition gene density per cell (not filtered) |
Split by condition gene density per cell (not filtered). PDF format |
raw_gene_dnst_spl_by_cond_plot_png | File (Optional) | Split by condition gene density per cell (not filtered) |
Split by condition gene density per cell (not filtered). PNG format |
fltr_gene_dnst_spl_by_cond_plot_pdf | File (Optional) | Split by condition gene density per cell (filtered) |
Split by condition gene density per cell (filtered). PDF format |
fltr_gene_dnst_spl_by_cond_plot_png | File (Optional) | Split by condition gene density per cell (filtered) |
Split by condition gene density per cell (filtered). PNG format |
raw_gene_umi_corr_spl_by_ident_plot_pdf | File (Optional) | Split by identity genes vs UMIs per cell correlation (not filtered) |
Split by identity genes vs UMIs per cell correlation (not filtered). PDF format |
raw_gene_umi_corr_spl_by_ident_plot_png | File (Optional) | Split by identity genes vs UMIs per cell correlation (not filtered) |
Split by identity genes vs UMIs per cell correlation (not filtered). PNG format |
raw_mito_perc_dnst_spl_by_cond_plot_pdf | File (Optional) | Split by condition density of transcripts mapped to mitochondrial genes per cell (not filtered) |
Split by condition density of transcripts mapped to mitochondrial genes per cell (not filtered). PDF format |
raw_mito_perc_dnst_spl_by_cond_plot_png | File (Optional) | Split by condition density of transcripts mapped to mitochondrial genes per cell (not filtered) |
Split by condition density of transcripts mapped to mitochondrial genes per cell (not filtered). PNG format |
fltr_gene_umi_corr_spl_by_ident_plot_pdf | File (Optional) | Split by identity genes vs UMIs per cell correlation (filtered) |
Split by identity genes vs UMIs per cell correlation (filtered). PDF format |
fltr_gene_umi_corr_spl_by_ident_plot_png | File (Optional) | Split by identity genes vs UMIs per cell correlation (filtered) |
Split by identity genes vs UMIs per cell correlation (filtered). PNG format |
fltr_mito_perc_dnst_spl_by_cond_plot_pdf | File (Optional) | Split by condition density of transcripts mapped to mitochondrial genes per cell (filtered) |
Split by condition density of transcripts mapped to mitochondrial genes per cell (filtered). PDF format |
fltr_mito_perc_dnst_spl_by_cond_plot_png | File (Optional) | Split by condition density of transcripts mapped to mitochondrial genes per cell (filtered) |
Split by condition density of transcripts mapped to mitochondrial genes per cell (filtered). PNG format |
raw_nvlt_score_dnst_spl_by_cond_plot_pdf | File (Optional) | Split by condition novelty score density per cell (not filtered) |
Split by condition novelty score density per cell (not filtered). PDF format |
raw_nvlt_score_dnst_spl_by_cond_plot_png | File (Optional) | Split by condition novelty score density per cell (not filtered) |
Split by condition novelty score density per cell (not filtered). PNG format |
fltr_nvlt_score_dnst_spl_by_cond_plot_pdf | File (Optional) | Split by condition novelty score density per cell (filtered) |
Split by condition novelty score density per cell (filtered). PDF format |
fltr_nvlt_score_dnst_spl_by_cond_plot_png | File (Optional) | Split by condition novelty score density per cell (filtered) |
Split by condition novelty score density per cell (filtered). PNG format |
https://w3id.org/cwl/view/git/480e99a4bb3046e0565113d9dca294e0895d3b0c/workflows/seurat-cluster.cwl